One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/11/25/peak-motifs.2025-11-25.143236_2025-11-25.143236_C5OFib/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2.tf -format2 tf -file2 $RSAT/public_html/motif_databases/JASPAR/Jaspar_2024/JASPAR2024_CORE_vertebrates_non-redundant_pfms_transfac.txt -mode matches -strand DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.7 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,width,strand,offset,alignments_1ton -sort Ncor -quick -o $RSAT/public_html/tmp/www-data/2025/11/25/peak-motifs.2025-11-25.143236_2025-11-25.143236_C5OFib/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2_vs_db_JASPAR2024_CORE_vertebrates_non-redundant

One-to-n matrix alignment; reference matrix: positions_6nt_m2_shift6 ; 12 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m2_shift6 (positions_6nt_m2)
; positions_6nt_m2; m=0 (reference); ncol1=11; shift=6; ncol=17; ------wwCCCCTTAwh ; Alignment reference a 0 0 0 0 0 0 1279 1282 330 190 247 317 365 181 3656 1030 1099 c 0 0 0 0 0 0 608 697 2744 3508 3434 3235 139 61 61 824 1116 g 0 0 0 0 0 0 729 669 314 35 57 51 118 43 35 754 504 t 0 0 0 0 0 0 1251 1219 479 134 129 264 3245 3582 115 1259 1148

MA0122.4_shift6 (Nkx3-2)
; positions_6nt_m2 versus MA0122.4 (Nkx3-2); m=1/11; ncol2=10; w=0; offset=0; strand=D; shift=6; score=0.695855; ------aamCACTTAa- ; cor=; Ncor= a 0 0 0 0 0 0 5714.0 5598.0 2604.0 79.0 9907.0 151.0 50.0 95.0 9680.0 5620.0 0 c 0 0 0 0 0 0 952.0 1109.0 5079.0 9900.0 82.0 9965.0 32.0 138.0 147.0 991.0 0 g 0 0 0 0 0 0 1466.0 1154.0 1504.0 23.0 19.0 10.0 29.0 68.0 68.0 1368.0 0 t 0 0 0 0 0 0 2088.0 2359.0 1033.0 218.0 212.0 94.0 10109.0 9919.0 325.0 2241.0 0

MA0124.3_shift8 (Nkx3-1)
; positions_6nt_m2 versus MA0124.3 (Nkx3-1); m=2/11; ncol2=7; w=0; offset=2; strand=D; shift=8; score=0.495266; --------cCACTTA-- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 981.0 0.0 5335.0 59.0 0.0 0.0 5335.0 0 0 c 0 0 0 0 0 0 0 0 5335.0 5335.0 28.0 5335.0 1.0 254.0 273.0 0 0 g 0 0 0 0 0 0 0 0 1776.0 10.0 10.0 9.0 0.0 0.0 173.0 0 0 t 0 0 0 0 0 0 0 0 275.0 336.0 88.0 9.0 5335.0 5335.0 523.0 0 0

MA0482.3_shift10 (GATA4)
; positions_6nt_m2 versus MA0482.3 (GATA4); m=3/11; ncol2=8; w=0; offset=4; strand=D; shift=10; score=0.479321; ----------cCTTATC ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 3977.0 3150.0 1586.0 1650.0 54420.0 770.0 480.0 c 0 0 0 0 0 0 0 0 0 0 38289.0 50062.0 1429.0 1377.0 1703.0 582.0 56544.0 g 0 0 0 0 0 0 0 0 0 0 5099.0 1103.0 749.0 808.0 1245.0 539.0 568.0 t 0 0 0 0 0 0 0 0 0 0 11649.0 4699.0 55250.0 55179.0 1646.0 57123.0 1422.0

MA1608.2_shift9 (Isl1)
; positions_6nt_m2 versus MA1608.2 (Isl1); m=4/11; ncol2=7; w=0; offset=3; strand=D; shift=9; score=0.478611; ---------CCATTAg- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 356.0 432.0 5476.0 67.0 64.0 5462.0 1089.0 0 c 0 0 0 0 0 0 0 0 0 4710.0 4885.0 30.0 54.0 104.0 45.0 410.0 0 g 0 0 0 0 0 0 0 0 0 192.0 54.0 99.0 34.0 39.0 20.0 3702.0 0 t 0 0 0 0 0 0 0 0 0 379.0 266.0 32.0 5482.0 5430.0 110.0 436.0 0

MA1545.2_shift8 (OVOL2)
; positions_6nt_m2 versus MA1545.2 (OVOL2); m=5/11; ncol2=7; w=0; offset=2; strand=D; shift=8; score=0.450066; --------aCCGTTA-- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 8885.0 3.0 0.0 0.0 0.0 0.0 12491.0 0 0 c 0 0 0 0 0 0 0 0 1602.0 12491.0 12491.0 0.0 1402.0 0.0 13.0 0 0 g 0 0 0 0 0 0 0 0 450.0 24.0 41.0 12491.0 0.0 9.0 151.0 0 0 t 0 0 0 0 0 0 0 0 3607.0 0.0 0.0 0.0 12491.0 12491.0 0.0 0 0

MA1117.2_shift5 (RELB)
; positions_6nt_m2 versus MA1117.2 (RELB); m=6/11; ncol2=7; w=-1; offset=-1; strand=D; shift=5; score=0.429345; -----ATTCCCC----- ; cor=; Ncor= a 0 0 0 0 0 2833.0 210.0 90.0 144.0 92.0 146.0 79.0 0 0 0 0 0 c 0 0 0 0 0 127.0 107.0 103.0 2928.0 3098.0 3013.0 3035.0 0 0 0 0 0 g 0 0 0 0 0 157.0 159.0 53.0 40.0 28.0 58.0 107.0 0 0 0 0 0 t 0 0 0 0 0 173.0 2814.0 3044.0 178.0 72.0 73.0 69.0 0 0 0 0 0

MA1578.2_shift6 (VEZF1)
; positions_6nt_m2 versus MA1578.2 (VEZF1); m=7/11; ncol2=6; w=0; offset=0; strand=D; shift=6; score=0.423548; ------CCCCCC----- ; cor=; Ncor= a 0 0 0 0 0 0 71.0 1.0 4.0 2.0 6.0 10.0 0 0 0 0 0 c 0 0 0 0 0 0 790.0 997.0 995.0 997.0 989.0 977.0 0 0 0 0 0 g 0 0 0 0 0 0 137.0 0.0 0.0 0.0 0.0 3.0 0 0 0 0 0 t 0 0 0 0 0 0 0.0 0.0 0.0 0.0 4.0 8.0 0 0 0 0 0

MA0056.3_shift5 (MZF1)
; positions_6nt_m2 versus MA0056.3 (MZF1); m=8/11; ncol2=8; w=-1; offset=-1; strand=D; shift=5; score=0.420223; -----AATCCCCA---- ; cor=; Ncor= a 0 0 0 0 0 5855.0 7149.0 106.0 100.0 135.0 111.0 117.0 6036.0 0 0 0 0 c 0 0 0 0 0 1016.0 426.0 56.0 7949.0 7939.0 7919.0 7673.0 611.0 0 0 0 0 g 0 0 0 0 0 999.0 385.0 98.0 100.0 54.0 58.0 83.0 484.0 0 0 0 0 t 0 0 0 0 0 372.0 282.0 7982.0 93.0 114.0 154.0 369.0 1111.0 0 0 0 0

MA0766.3_rc_shift10 (GATA5_rc)
; positions_6nt_m2 versus MA0766.3_rc (GATA5_rc); m=9/11; ncol2=8; w=0; offset=4; strand=R; shift=10; score=0.413754; ----------ysTTATC ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 668.0 586.0 204.0 331.0 15369.0 0.0 0.0 c 0 0 0 0 0 0 0 0 0 0 8179.0 7774.0 200.0 0.0 0.0 0.0 15369.0 g 0 0 0 0 0 0 0 0 0 0 3215.0 7594.0 0.0 0.0 0.0 0.0 0.0 t 0 0 0 0 0 0 0 0 0 0 7190.0 212.0 15369.0 15369.0 0.0 15369.0 0.0

MA0036.4_shift11 (GATA2)
; positions_6nt_m2 versus MA0036.4 (GATA2); m=10/11; ncol2=7; w=0; offset=5; strand=D; shift=11; score=0.410576; -----------CTTATC ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 940.0 444.0 417.0 14098.0 145.0 96.0 c 0 0 0 0 0 0 0 0 0 0 0 10607.0 259.0 34.0 14.0 77.0 13786.0 g 0 0 0 0 0 0 0 0 0 0 0 1223.0 150.0 21.0 43.0 48.0 126.0 t 0 0 0 0 0 0 0 0 0 0 0 1443.0 13360.0 13741.0 58.0 13943.0 205.0

MA1600.2_shift0 (ZNF684)
; positions_6nt_m2 versus MA1600.2 (ZNF684); m=11/11; ncol2=14; w=-6; offset=-6; strand=D; shift=0; score=0.40504; ACAGTCCACCCCTT--- ; cor=; Ncor= a 1238.0 9.0 1184.0 60.0 9.0 13.0 40.0 1012.0 3.0 44.0 7.0 0.0 249.0 56.0 0 0 0 c 24.0 1253.0 11.0 216.0 14.0 1236.0 1221.0 9.0 1226.0 1253.0 1229.0 1263.0 129.0 59.0 0 0 0 g 68.0 9.0 110.0 1135.0 59.0 25.0 2.0 57.0 63.0 10.0 7.0 0.0 18.0 14.0 0 0 0 t 19.0 19.0 131.0 74.0 1259.0 10.0 67.0 220.0 61.0 6.0 92.0 3.0 1107.0 1224.0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6nt_m2_shift6 (positions_6nt_m2)				; positions_6nt_m2; m=0 (reference); ncol1=11; shift=6; ncol=17; ------wwCCCCTTAwh ; Alignment reference a 0 0 0 0 0 0 1279 1282 330 190 247 317 365 181 3656 1030 1099 c 0 0 0 0 0 0 608 697 2744 3508 3434 3235 139 61 61 824 1116 g 0 0 0 0 0 0 729 669 314 35 57 51 118 43 35 754 504 t 0 0 0 0 0 0 1251 1219 479 134 129 264 3245 3582 115 1259 1148
MA0122.4_shift6 (Nkx3-2)				; positions_6nt_m2 versus MA0122.4 (Nkx3-2); m=1/11; ncol2=10; w=0; offset=0; strand=D; shift=6; score=0.695855; ------aamCACTTAa- ; cor=; Ncor= a 0 0 0 0 0 0 5714.0 5598.0 2604.0 79.0 9907.0 151.0 50.0 95.0 9680.0 5620.0 0 c 0 0 0 0 0 0 952.0 1109.0 5079.0 9900.0 82.0 9965.0 32.0 138.0 147.0 991.0 0 g 0 0 0 0 0 0 1466.0 1154.0 1504.0 23.0 19.0 10.0 29.0 68.0 68.0 1368.0 0 t 0 0 0 0 0 0 2088.0 2359.0 1033.0 218.0 212.0 94.0 10109.0 9919.0 325.0 2241.0 0
MA0124.3_shift8 (Nkx3-1)				; positions_6nt_m2 versus MA0124.3 (Nkx3-1); m=2/11; ncol2=7; w=0; offset=2; strand=D; shift=8; score=0.495266; --------cCACTTA-- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 981.0 0.0 5335.0 59.0 0.0 0.0 5335.0 0 0 c 0 0 0 0 0 0 0 0 5335.0 5335.0 28.0 5335.0 1.0 254.0 273.0 0 0 g 0 0 0 0 0 0 0 0 1776.0 10.0 10.0 9.0 0.0 0.0 173.0 0 0 t 0 0 0 0 0 0 0 0 275.0 336.0 88.0 9.0 5335.0 5335.0 523.0 0 0
MA0482.3_shift10 (GATA4)				; positions_6nt_m2 versus MA0482.3 (GATA4); m=3/11; ncol2=8; w=0; offset=4; strand=D; shift=10; score=0.479321; ----------cCTTATC ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 3977.0 3150.0 1586.0 1650.0 54420.0 770.0 480.0 c 0 0 0 0 0 0 0 0 0 0 38289.0 50062.0 1429.0 1377.0 1703.0 582.0 56544.0 g 0 0 0 0 0 0 0 0 0 0 5099.0 1103.0 749.0 808.0 1245.0 539.0 568.0 t 0 0 0 0 0 0 0 0 0 0 11649.0 4699.0 55250.0 55179.0 1646.0 57123.0 1422.0
MA1608.2_shift9 (Isl1)				; positions_6nt_m2 versus MA1608.2 (Isl1); m=4/11; ncol2=7; w=0; offset=3; strand=D; shift=9; score=0.478611; ---------CCATTAg- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 356.0 432.0 5476.0 67.0 64.0 5462.0 1089.0 0 c 0 0 0 0 0 0 0 0 0 4710.0 4885.0 30.0 54.0 104.0 45.0 410.0 0 g 0 0 0 0 0 0 0 0 0 192.0 54.0 99.0 34.0 39.0 20.0 3702.0 0 t 0 0 0 0 0 0 0 0 0 379.0 266.0 32.0 5482.0 5430.0 110.0 436.0 0
MA1545.2_shift8 (OVOL2)				; positions_6nt_m2 versus MA1545.2 (OVOL2); m=5/11; ncol2=7; w=0; offset=2; strand=D; shift=8; score=0.450066; --------aCCGTTA-- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 8885.0 3.0 0.0 0.0 0.0 0.0 12491.0 0 0 c 0 0 0 0 0 0 0 0 1602.0 12491.0 12491.0 0.0 1402.0 0.0 13.0 0 0 g 0 0 0 0 0 0 0 0 450.0 24.0 41.0 12491.0 0.0 9.0 151.0 0 0 t 0 0 0 0 0 0 0 0 3607.0 0.0 0.0 0.0 12491.0 12491.0 0.0 0 0
MA1117.2_shift5 (RELB)				; positions_6nt_m2 versus MA1117.2 (RELB); m=6/11; ncol2=7; w=-1; offset=-1; strand=D; shift=5; score=0.429345; -----ATTCCCC----- ; cor=; Ncor= a 0 0 0 0 0 2833.0 210.0 90.0 144.0 92.0 146.0 79.0 0 0 0 0 0 c 0 0 0 0 0 127.0 107.0 103.0 2928.0 3098.0 3013.0 3035.0 0 0 0 0 0 g 0 0 0 0 0 157.0 159.0 53.0 40.0 28.0 58.0 107.0 0 0 0 0 0 t 0 0 0 0 0 173.0 2814.0 3044.0 178.0 72.0 73.0 69.0 0 0 0 0 0
MA1578.2_shift6 (VEZF1)				; positions_6nt_m2 versus MA1578.2 (VEZF1); m=7/11; ncol2=6; w=0; offset=0; strand=D; shift=6; score=0.423548; ------CCCCCC----- ; cor=; Ncor= a 0 0 0 0 0 0 71.0 1.0 4.0 2.0 6.0 10.0 0 0 0 0 0 c 0 0 0 0 0 0 790.0 997.0 995.0 997.0 989.0 977.0 0 0 0 0 0 g 0 0 0 0 0 0 137.0 0.0 0.0 0.0 0.0 3.0 0 0 0 0 0 t 0 0 0 0 0 0 0.0 0.0 0.0 0.0 4.0 8.0 0 0 0 0 0
MA0056.3_shift5 (MZF1)				; positions_6nt_m2 versus MA0056.3 (MZF1); m=8/11; ncol2=8; w=-1; offset=-1; strand=D; shift=5; score=0.420223; -----AATCCCCA---- ; cor=; Ncor= a 0 0 0 0 0 5855.0 7149.0 106.0 100.0 135.0 111.0 117.0 6036.0 0 0 0 0 c 0 0 0 0 0 1016.0 426.0 56.0 7949.0 7939.0 7919.0 7673.0 611.0 0 0 0 0 g 0 0 0 0 0 999.0 385.0 98.0 100.0 54.0 58.0 83.0 484.0 0 0 0 0 t 0 0 0 0 0 372.0 282.0 7982.0 93.0 114.0 154.0 369.0 1111.0 0 0 0 0
MA0766.3_rc_shift10 (GATA5_rc)				; positions_6nt_m2 versus MA0766.3_rc (GATA5_rc); m=9/11; ncol2=8; w=0; offset=4; strand=R; shift=10; score=0.413754; ----------ysTTATC ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 668.0 586.0 204.0 331.0 15369.0 0.0 0.0 c 0 0 0 0 0 0 0 0 0 0 8179.0 7774.0 200.0 0.0 0.0 0.0 15369.0 g 0 0 0 0 0 0 0 0 0 0 3215.0 7594.0 0.0 0.0 0.0 0.0 0.0 t 0 0 0 0 0 0 0 0 0 0 7190.0 212.0 15369.0 15369.0 0.0 15369.0 0.0
MA0036.4_shift11 (GATA2)				; positions_6nt_m2 versus MA0036.4 (GATA2); m=10/11; ncol2=7; w=0; offset=5; strand=D; shift=11; score=0.410576; -----------CTTATC ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 940.0 444.0 417.0 14098.0 145.0 96.0 c 0 0 0 0 0 0 0 0 0 0 0 10607.0 259.0 34.0 14.0 77.0 13786.0 g 0 0 0 0 0 0 0 0 0 0 0 1223.0 150.0 21.0 43.0 48.0 126.0 t 0 0 0 0 0 0 0 0 0 0 0 1443.0 13360.0 13741.0 58.0 13943.0 205.0
MA1600.2_shift0 (ZNF684)				; positions_6nt_m2 versus MA1600.2 (ZNF684); m=11/11; ncol2=14; w=-6; offset=-6; strand=D; shift=0; score=0.40504; ACAGTCCACCCCTT--- ; cor=; Ncor= a 1238.0 9.0 1184.0 60.0 9.0 13.0 40.0 1012.0 3.0 44.0 7.0 0.0 249.0 56.0 0 0 0 c 24.0 1253.0 11.0 216.0 14.0 1236.0 1221.0 9.0 1226.0 1253.0 1229.0 1263.0 129.0 59.0 0 0 0 g 68.0 9.0 110.0 1135.0 59.0 25.0 2.0 57.0 63.0 10.0 7.0 0.0 18.0 14.0 0 0 0 t 19.0 19.0 131.0 74.0 1259.0 10.0 67.0 220.0 61.0 6.0 92.0 3.0 1107.0 1224.0 0 0 0